I think Clemson and Alabama are two totally different games. The Clemson Offensive line is not great. They would have issues with the ND Defensive line. I think that's a battle ND wins and it puts the Clemson freshman QB under pressure all day, and Clemson is having issues running the ball lately. They scored in the mid 20's vs Syracuse and Texas AM and the ND defense is better. I think ND holds them to the low 20's/high teens. On the other side of the ball, their secondary is average at best. If the offensive line can give Book a little time, I think the passing game would have a field day. I think ND is a bad match up for Clemson and ND wins that game.
Alabama is obviously a different story. I do think the ND defensive line would be fine and limit the Alabama running game to 200 yards, and the LB's/secondary match up well. To keep them in check, a team needs to limit "Bama to long drives and stay away for the big play. Easier said than done, but ND has high draft NFL talent at all three levels (Tillary, Coney, and Love - all probable day 1 draft guys). It'd be hard to think that a team that has a potential first round draft pick at each level couldn't defensively compete. (Not mentioning Tranquil could be a day 2 draft guy and Gilliam a day 3 guy). ND's secondary is physical enough to get their hands on "Bama receivers, which you have to do to re-route them and mess with their Tua timing.
Offensively, I think the ND offense would be OK. If 'Bama has any issues its on defense. Their D-line is very good, but not great and their secondary is susceptible. To beat them, you have to pass the ball (not sure I'd go 85/15 - but maybe 25/75 to keep them honest), and stay away from their LB's. With Books short game accuracy, their DB's need to play up and that leaves them open to deep balls. Most teams that have beat them, have beat them through the air and have had big play success.
Clemson - (60%) I think ND is a bad match up for Clemson
Alabama - (20%) I think its a better game than people think